In case you hadn't seen my reply on an older exhaust thread and haven't already made a decision I hope this may be of some help:
Suitcase Muffler Delete - OEM Exhaust
Keep in mind that on both of my videos I was going wide-open throttle so it could be heard.
I don't have to do emissions testing in Alabama but I wouldn't see it causing that problem as I didn't remove any type of catalytic converter in the process.
As for the second part of your question, no, no check engine light has come on and I've driven over 2,000 miles with this setup now...
No problem! I think it'll make the motor easier to hear. There's a lot more sound on acceleration but it drops off steadily as you get up to speed. Mine is welded on. The local exhaust shop did everything for $60.
While there are a lot of options out there I ended up just having the suitcase (middle) muffler cut and replaced with a straight pipe. I had the shop leave the cylindrical resonator (front) and rear back baffle/resonator/muffler (rear).
Videos for reference:
Revs and Acceleration
Jeep...